Encoding a Full Organism Genome on a Quantum Computer

Speaker: Dr Floyd Creevey (UoM)
Date: Thursday 1pm – 2pm AEST
Zoom: Click here to join the seminar

Abstract:
In order for quantum computers to reach their full potential in analysing genomic information – quantum bioinformatics – there is a clear need for scalable and general methods for encoding genomic data into quantum states. We have proposed and implemented a matrix product state (MPS) based method for achieving such encoding. The use case of genomic workflows, particularly the emergent fields of quantum pangenomics and phylogeny, was highlighted as a use case which relies on a robust data encoding scheme targeting current and near-term quantum systems. This study advances on the prior work by implementing tailored depth-reduction for circuits encoding genome read data, enabling the full encoding of the genome of the Hepatitis-Delta virus on a quantum computer. These methods are widely applicable to reducing the depth of preparation circuits for separable discrete data, particularly high-entropy data. The application readiness of the encoding is demonstrated by performing quantum sequence alignment (QSA) based on the formalism on a sample of reads prepared with the MPS method on quantum hardware. Validation using HPC simulation, and tests on physical quantum computers charters a path to full near-term utility of the method that generalises to the fault-tolerant quantum computing era.

Bio:
Floyd Creevey is a Research Fellow in Quantum Bioinformatics at the University of Melbourne. He completed his undergraduate degrees in Computer and Software Systems Engineering and Physics at QUT. He then went on to complete his PhD in Quantum Computing at the University of Melbourne in 2025 under the supervision of Prof. Lloyd Hollenberg and Prof. Martin Sevior. While finishing his PhD he began a collaboration with the Oxford Q4Bio team, and went to work at the Wellcome Sanger Institute, as a part of Dr. Sergii Strelchuk’s team in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge. He then returned to the University of Melbourne to finish his PhD and worked as a Research Fellow in Quantum Bioinformatics, while continuing the collaboration. After completing his PhD he moved to the UK to work full time on the Q4Bio project, leading one of the four research streams. While there he was also employed as a Retained Lecturer in Computer Science at Jesus College Oxford, and held an honorary position at the University of Melbourne. After the conclusion of the Q4Bio project he moved back to work as a Research Fellow in Quantum Bioinformatics at the University of Melbourne.